Using ProHits to Store, Annotate, and Analyze Affinity Purification–Mass Spectrometry (AP‐MS) Data

Guomin Liu1, Jianping Zhang1, Hyungwon Choi2, Jean‐Philippe Lambert1, Tharan Srikumar3, Brett Larsen1, Alexey I. Nesvizhskii4, Brian Raught3, Mike Tyers5, Anne‐Claude Gingras6

1 Centre for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, Ontario, Canada, 2 Saw Swee Hock School of Public Health, National University of Singapore, Singapore, 3 Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada, 4 Department of Pathology and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 5 Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada and Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom, 6 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 8.16
DOI:  10.1002/0471250953.bi0816s39
Online Posting Date:  September, 2012
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Affinity purification coupled with mass spectrometry (AP‐MS) is a robust technique used to identify protein‐protein interactions. With recent improvements in sample preparation, and dramatic advances in MS instrumentation speed and sensitivity, this technique is becoming more widely used throughout the scientific community. To meet the needs of research groups both large and small, we have developed software solutions for tracking, scoring and analyzing AP‐MS data. Here, we provide details for the installation and utilization of ProHits, a Laboratory Information Management System designed specifically for AP‐MS interaction proteomics. This protocol explains: (i) how to install the complete ProHits system, including modules for the management of mass spectrometry files and the analysis of interaction data, and (ii) alternative options for the use of pre‐existing search results in simpler versions of ProHits, including a virtual machine implementation of our ProHits Lite software. We also describe how to use the main features of the software to analyze AP‐MS data. Curr. Protoc. Bioinform. 39:8.16.1‐8.16.32. © 2012 by John Wiley & Sons, Inc.

Keywords: affinity purification coupled with mass spectrometry; data analysis; virtual machine; statistical models; protein‐protein interactions

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Table of Contents

  • Introduction
  • Basic Protocol 1: Installation of the Full Version of ProHits on a Linux Server
  • Alternate Protocol 1: Installing ProHits Lite on a Mac OS X or Windows PC via a Virtual Machine
  • Support Protocol 1: Setting Up Projects and Users in the Admin Office Module
  • Basic Protocol 2: Tracking Data in ProHits: Data Management Module
  • Basic Protocol 3: Analyzing AP‐MS Data: ProHits Analyst Module
  • Support Protocol 2: Managing Protocols and Lists in the Analyst Module
  • Commentary
  • Literature Cited
  • Figures
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Basic Protocol 1: Installation of the Full Version of ProHits on a Linux Server

  • Pre‐installed ProHits full version or Lite version, set up as in protocol 3
  • Web access via browser of choice
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Literature Cited

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Internet Resources
  ProHits source code.
  SAINT source code.
  Reference for the complete Cytoscape project.
  Cytoscape Web source code.
  BioGRID Web site for interactions.
  Source code for the ProteoWizard project; converters are used in ProHits.
  Trans Proteomic Pipeline project.
  X!Tandem open‐source search engine.
  NCBI RefSeq project.
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